// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
//\r
// Contact: phylosoft @ gmail . com\r
-// WWW: www.phylosoft.org/forester\r
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
\r
package org.forester.util;\r
\r
//Protein: 3 letters + 5 numerals\r
//http://www.ncbi.nlm.nih.gov/Sequin/acc.html\r
private final static Pattern GENBANK_NUCLEOTIDE_AC_PATTERN_1 = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5})(?:[^a-zA-Z0-9]|\\Z)" );\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
private final static Pattern GENBANK_NUCLEOTIDE_AC_PATTERN_2 = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6})(?:[^a-zA-Z0-9]|\\Z)" );\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
private final static Pattern GENBANK_PROTEIN_AC_PATTERN = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5})(?:[^a-zA-Z0-9]|\\Z)" );\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
// RefSeq accession numbers can be distinguished from GenBank accessions \r
// by their distinct prefix format of 2 characters followed by an\r
// underscore character ('_'). For example, a RefSeq protein accession is NP_015325. \r
private final static Pattern REFSEQ_PATTERN = Pattern\r
.compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
+ // See: http://web.expasy.org/docs/userman.html#ID_line\r
+ private final static Pattern TREMBL_PATTERN = Pattern\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z][0-9][A-Z0-9]{3}[0-9])(?:[^a-zA-Z0-9]|\\Z)" );\r
+ private final static Pattern GI_PATTERN = Pattern\r
+ .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
\r
/**\r
* Returns null if no match.\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
return new Identifier( v, Identifier.REFSEQ );\r
}\r
+ v = parseTrEMBLAccessor( s );\r
+ if ( !ForesterUtil.isEmpty( v ) ) {\r
+ return new Identifier( v, Identifier.SP );\r
+ }\r
return null;\r
}\r
\r
- public static boolean isProtein( final String query ) {\r
+ public final static boolean isProtein( final String query ) {\r
+ final String r1 = parseRefSeqAccessor( query );\r
+ if ( !ForesterUtil.isEmpty( r1 ) && ( r1.charAt( 1 ) == 'P' ) ) {\r
+ return true;\r
+ }\r
+ final String r2 = parseTrEMBLAccessor( query );\r
+ if ( !ForesterUtil.isEmpty( r2 ) ) {\r
+ return true;\r
+ }\r
return GENBANK_PROTEIN_AC_PATTERN.matcher( query ).lookingAt();\r
}\r
\r
* Returns null if no match.\r
* \r
*/\r
- private final static String parseRefSeqAccessor( final String query ) {\r
+ public final static String parseRefSeqAccessor( final String query ) {\r
final Matcher m = REFSEQ_PATTERN.matcher( query );\r
if ( m.lookingAt() ) {\r
return m.group( 1 );\r
return null;\r
}\r
\r
+ /**\r
+ * Returns null if no match.\r
+ * \r
+ */\r
+ private final static String parseTrEMBLAccessor( final String query ) {\r
+ final Matcher m = TREMBL_PATTERN.matcher( query );\r
+ if ( m.lookingAt() ) {\r
+ return m.group( 1 );\r
+ }\r
+ return null;\r
+ }\r
+\r
private SequenceIdParser() {\r
// Hiding the constructor.\r
}\r
+\r
+ public static String parseGInumber( final String query ) {\r
+ final Matcher m = GI_PATTERN.matcher( query );\r
+ if ( m.find() ) {\r
+ return m.group( 1 );\r
+ }\r
+ return null;\r
+ }\r
}\r